I think the planning would be a bit more overwhelming than in Europe, due to language, and the myriad of choices of transport and lodging Japan has. Just read that Tokyo is the world's largest city - 34 million. That's a lot of hotels and neighborhoods to choose from! There are multiple train, subway, bus, and metro systems that more or less work seamlessly together but require different tickets and reservations. I was glad to have our company do that leg work.
Our trip, for 10 days, that covered Tokyo, Nagoya (Ghibli Park tickets for one day), Takayama, Kanazawa, and Hiroshima, with at least one guided tour in each city, train and bus tickets, a pre-loaded subway card, lodging, and a pocket wifi was $5,500/person.
What we did not have was a full time, 24 hr access guide, someone to navigate you thru confusing train stations (google maps worked well for that,) meals included, and luggage handling/forwarding. Or a large group to travel with, with some people prefer.
Regarding luggage, if you travel by train, there is limited luggage space, and anything larger than a carryon needs a separate reservation for space. You also have drag all of that thru stations where the elevator/escalator may not be convenient to where you're going. Japan has a smooth system of luggage forwarding, with several companies that will pick up your luggage at your hotel and deliver to the next location the next day. We used this a few times. This means that you need a smaller bag, like your carry on, to use for the next 24 hours until your luggage shows up. Luggage forwarding can not be used to an airbnb, as they need a human to sign for it. You can also, usually, do this from/to airport locations as well.
I can see why the initial
ABD's used buses, so they didn't need to deal with this. If they are doing trains now, they're either going to make you forward your luggage at some point, or they've mass-reserved the luggage space.